Presentation for bioassit lectures.

• Molgenis semantic
  • According to ​http://www.molgenis.org/wiki/AddingDataTypes
    • added in molgenis_db.xml : 

          <entity name="OntologyTerm">
                  <description>
                      The OntologyTerm class defines references to a single entry from an ontology or a controlled vocabulary. Other classes can reference to
                      this OntologyTerm to harmonize naming of concepts. Each term should have a local, unique label. Good practice is to label it 'sourceid:term', e.g.
                      'MO:cell' If no suitable ontology term exists one can define new terms locally in which case there is no formal accession for the term. In those
                      cases the local name should be repeated in both term and termAccession. Maps to FuGE::OntologyIndividual; in MAGE-TAB there is no separate entity to
                      model terms.
          	Should this be extending or implement smthg?
          
                  </description>
           		<field name="id" type="autoid"/>
                  <field nillable="false" auto="false" name="term" type="varchar"
                   description="The ontology term itself, also known as the 'local name' in some ontologies."/>
                  <field name="description" type="text"
                   description="Definition of the term." nillable="true"/>
       			<field nillable="true" auto="false" name="termAccession" type="varchar"
                   description="The accession number assigned to the ontology term in the source ontology. If empty it is assumed to be a locally defined term. "/>
                  <field auto="false" name="termSource" type="xref"
                   description="The source ontology or controlled vocabulary list that ontology terms have been obtained from. One can define a local ontology if needed."
                   xref_field="OntologySource.id" xref_label="name"/>
                  <unique fields="termSource,term"
                   description="the local label of the OntologyTerm is unique within a data set."/>
              </entity>	
          
      

• test servlet for decorator. ​http://www.molgenis.org/wiki/MolgenisServletDecorator

• skype on biobank hackathon :

Wendesday 6/10/2010

demo seems to be working 
do more 
or leave it this way until the conference 

Latest Peregrine: Precision=0.7797356828193832 Recall=0.6764331210191082 F-measure= 0.7244201909959072
[10/6/10 3:16:15 PM] Reinout van Schouwen: Let me try to fix my sound... back in a sec


what about the language that appears in the left panel when the article is not english . --> still english . 

issues (after the demo) :

pop up in left panel (get it working) 
internationalization 
separate bionanks with medlines or different language biobanks

still the error (from nbic site)

get rid of the pop up   (seems distracting)

people (in the accordion) are not links 

concepts are outside the accordion 

for  http://www.ncbi.nlm.nih.gov/pubmed/11254977: internal error 

rack space / cloud server , expensive machine , pay by the hour , turn it off is an option ?

tokenizer for different problems ? depends (LEON)

for now and on , resolve the issues above, shut it down , fire it up before demo . 

No next Skype arranged.